To illustrate the power of COD in elucidating the dynamics behind protein complexes, we consider the TNFα/NF-κB signaling pathway. The Nuclear Factor κB (NF-κB) family of transcription factors is activated in response to a diverse set of stress stimuli, which includes pro-inflammatory cytokines, e.g., TNFα. In vertebrates, this family includes p50, p52, Rel A, c-Rel, and Rel B, which bind to the DNA in a homo or heterodimeric fashion. The NF-κB activity is regulated by the IκB family of proteins via inhibitory ankyrin repeat domains. This family includes IκBα, IκBβ, and IκB∈. The precursors of p50 (p105) and p52 (pl00) also possess ankyrin repeat domains and thus act as inhibitors. These precursors can also form dimers with other members of the NF-κB family. The activation with the pro-inflammatory cytokine tumor necrosis factor TNFα triggers a signaling cascade, which, in particular, stimulates the activation of the IKKα, IKKβ, and IKKγ functional groups. The IKKs initiate a signal induced degradation of the inhibitors (IκBs), and subsequent nuclear translocation of the transcription factor. Recent TAP experiments [5] provide a wealth of new information regarding this important signaling pathway. Bouwmeester et al. identified 221 molecular associations, out of which only 80 where previously known. Gagneur et al. [16] applied modular decomposition to the network of these associations but the decomposition halted quickly at large non-decomposable modules.